Scott Dixon led the way for Ganassi in the final Carb Day practice ahead of Sunday's Indianapolis 500.
The 2008 race winner set a best speed of 225.474mph in the traditional one-hour morning session at the speedway.
Ganassi held a one-two for a long while, with Dario Franchitti second behind his team-mate.
But in the closing stages polesitter Alex Tagliani (Sam Schmidt Motorsports) steadily moved forwarded until he ended up splitting the Ganassi duo.
AJ Foyt Racing had a very strong session, with Vitor Meira fourth and his one-off team-mate Ryan Hunter-Reay - who took over Bruno Junqueira's car after failing to qualify his Andretti Autosport entry - taking seventh on his return to the squad.
They were split by Bryan Herta Autosport's Dan Wheldon and Panther Racing's Buddy Rice.
Tony Kanaan (KV), Helio Castroneves (Penske) and John Andretti (Andretti) completed the top 10.
Pos Driver Team Time Gap 1. Scott Dixon Ganassi 39.9159s 2. Alex Tagliani Sam Schmidt 40.0464s + 0.1305s 3. Dario Franchitti Ganassi 40.0609s + 0.1450s 4. Vitor Meira Foyt 40.0927s + 0.1768s 5. Dan Wheldon Herta 40.0999s + 0.1840s 6. Buddy Rice Panther 40.1054s + 0.1895s 7. Ryan Hunter-Reay Foyt 40.1912s + 0.2753s 8. Tony Kanaan KV 40.2022s + 0.2863s 9. Helio Castroneves Penske 40.2035s + 0.2876s 10. John Andretti Petty/Andretti 40.2051s + 0.2892s 11. JR Hildebrand Panther 40.2091s + 0.2932s 12. Townsend Bell Sam Schmidt 40.2130s + 0.2971s 13. Will Power Penske 40.2180s + 0.3021s 14. Graham Rahal Ganassi 40.2825s + 0.3666s 15. Ryan Briscoe Penske 40.2914s + 0.3755s 16. Ed Carpenter Sarah Fisher 40.3188s + 0.4029s 17. Paul Tracy Dreyer & Reinbold 40.3206s + 0.4047s 18. Justin Wilson Dreyer & Reinbold 40.3299s + 0.4140s 19. Jay Howard Rahal/Schmidt 40.3514s + 0.4355s 20. Danica Patrick Andretti 40.3897s + 0.4738s 21. Alex Lloyd Dale Coyne 40.3992s + 0.4833s 22. Simona de Silvestro HVM 40.4067s + 0.4908s 23. Bertrand Baguette Rahal Letterman Lanigan 40.4171s + 0.5012s 24. Ana Beatriz Dreyer & Reinbold 40.4312s + 0.5153s 25. James Hinchcliffe Newman/Haas 40.4615s + 0.5456s 26. Charlie Kimball Ganassi 40.4944s + 0.5785s 27. Davey Hamilton Dreyer & Reinbold 40.5099s + 0.5940s 28. Oriol Servia Newman/Haas 40.5104s + 0.5945s 29. Marco Andretti Andretti 40.5724s + 0.6565s 30. Pippa Mann Conquest 40.7441s + 0.8282s 31. Tomas Scheckter KV/SH 40.8201s + 0.9042s 32. EJ Viso KV 40.9436s + 1.0277s 33. Takuma Sato KV 43.4321s + 3.5162s